Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PPARA

Cell type

Cell type Class
Liver
Cell type
Hep G2
Primary Tissue
Liver
Tissue Diagnosis
Carcinoma Hepatocellular

Attributes by original data submitter

Sample

source_name
HEPG2 cells
cell line
HEPG2
treatment
Transfection with PPARa+ Estrogen receptor alpha and treated with their respective agonist.
agonist
PPARa agonist Wy13643 + Ea stimulated agonist PPT
chip antibody
anti-PPAR alpha antibody (Abcam, Catalog No.- ab227074, Lot name- GR3201839-22)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
SimpleChIP Enzymatic Chromatin IP kit (CST) was used for immunoprecipitation following manufacturer's instruction. Cells were washed with ice cold PBS twice and then crosslinked by incubating with 1% formaldehyde for 10 min. The reaction was stopped by the addition of 2.5 M glycine and the plates were washed twice with ice cold PBS. Chromatin was treated with nuclease and subjected to sonication. Immunoprecipitation was performed with PPARα specific antibody (Abcam ChIP-grade ab227074) and Protein G magnetic beads. Chromatin was eluted from the beads, uncrosslinked and purified. ChIP and input DNA libraries were prepared using Clontech DNA SMART kit (Takara Bio 634866).

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
25734659
Reads aligned (%)
88.2
Duplicates removed (%)
6.1
Number of peaks
245740 (qval < 1E-05)

hg19

Number of total reads
25734659
Reads aligned (%)
88.0
Duplicates removed (%)
6.2
Number of peaks
243866 (qval < 1E-05)

Base call quality data from DBCLS SRA